An Explainable-AI approach for Diagnosis of COVID-19 using MALDI-ToF Mass Spectrometry

The novel severe acute respiratory syndrome coronavirus type-2 (SARS-CoV-2) caused a global pandemic that has taken more than 4.5 million lives and severely affected the global economy. To curb the spread of the virus, an accurate, cost-effective, and quick testing for large populations is exceedingly important in order to identify, isolate, and treat infected people. Current testing methods commonly use PCR (Polymerase Chain Reaction) based equipment that have limitations on throughput, cost-effectiveness, and simplicity of procedure which creates a compelling need for developing additional coronavirus disease-2019 (COVID-19) testing mechanisms, that are highly sensitive, rapid, trustworthy, and convenient to use by the public. We propose a COVID-19 testing method using artificial intelligence (AI) techniques on MALDI-ToF (matrix-assisted laser desorption/ionization time-of-flight) data extracted from 152 human gargle samples (60 COVID-19 positive tests and 92 COVID-19 negative tests). Our AI-based approach leverages explainable-AI (X-AI) methods to explain the decision rules behind the predictive algorithm both on a local (per-sample) and global (all-samples) basis to make the AI model more trustworthy. Finally, we evaluated our proposed method using a 70%-30% train-test-split strategy and achieved a training accuracy of 86.79% and a testing accuracy of 91.30%.